I'm behind in recent year's prog, but I can say that there are great counterpoints in classic prog, a clear case being classic Yes. In CTTE for example there are quite some phrases which are at some initial point played on their own but then get assembled together being transposed or combined to form complex melodical and harmonical textures.
Classic Genesis had quite a few of these too.
Funnily ELP, as classically influenced as they were had less of this type of counterpoint, but they explored more the actual fugue pattern like in The Only Way or Trilogy's Fugue.
A Fugue is a more specific musical figure in which a melodical pattern is repeated starting in different beats of the bar, or in the next bar, creating a complex harmonic soundscape. Indeed ELP's The Only Way or Trilogy's Fugue are examples of it.
In a more modern environment, Yes's 91205 has some great counterpoint parts.